Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008350.1 Hibiscus syriacus cultivar Beakdansim tig00111084_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 573897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:389562 original size:31 final size:31
Alignment explanation
Indices: 389519--389579 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
389509 AAACTTAAAA
* *
389519 TAGTTTTGCAATAATGAGATTTAAATAATTT
1 TAGTTTTACAATAATGAAATTTAAATAATTT
*
389550 TAGTTTTACAATACTGAAATTTAAATAATT
1 TAGTTTTACAATAATGAAATTTAAATAATT
389580 CATTAAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
TAGTTTTACAATAATGAAATTTAAATAATTT
Found at i:389628 original size:22 final size:22
Alignment explanation
Indices: 389603--389645 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
389593 TAATAAATTA
389603 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
389625 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATCTATA
389646 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:389654 original size:22 final size:22
Alignment explanation
Indices: 389605--389653 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
389595 ATAAATTATT
**
389605 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCTATATAA
389627 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATA-TAA
389650 TAAA
1 TAAA
389654 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:389663 original size:32 final size:30
Alignment explanation
Indices: 389625--389758 Score: 114
Period size: 30 Copynumber: 4.3 Consensus size: 30
389615 CAATCTATAT
389625 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAAT-AATCTATA-TAATAAATTA
*
389657 TTTAAAATAAATCAATCCATATTTTATAATAATTTA
1 TTTAAAATAAAT-AAT-C-TA---TATAATAAATTA
* *
389693 TTTCAAAATAAATTAT-TTTATAATAAATTA
1 TTT-AAAATAAATAATCTATATAATAAATTA
*
389723 TTTTAAAATAAATAACCT-TAT--TAAATTA
1 -TTTAAAATAAATAATCTATATAATAAATTA
389751 TTTAAAAT
1 TTTAAAAT
389759 TATTTTAATA
Statistics
Matches: 88, Mismatches: 6, Indels: 21
0.77 0.05 0.18
Matches are distributed among these distances:
27 8 0.09
28 7 0.08
30 24 0.27
31 4 0.05
32 16 0.18
33 2 0.02
34 2 0.02
36 14 0.16
37 11 0.12
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTAAAATAAATAATCTATATAATAAATTA
Found at i:389702 original size:15 final size:15
Alignment explanation
Indices: 389676--389735 Score: 84
Period size: 15 Copynumber: 4.0 Consensus size: 15
389666 AATCAATCCA
* *
389676 TATTTTATAATAATT
1 TATTTTAAAATAAAT
*
389691 TATTTCAAAATAAAT
1 TATTTTAAAATAAAT
*
389706 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
389721 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
389736 AACCTTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:392987 original size:2 final size:2
Alignment explanation
Indices: 392980--393030 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
392970 TATAAAAGAA
392980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
393022 AT AT AT AT A
1 AT AT AT AT A
393031 CATTCTATGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:397735 original size:30 final size:31
Alignment explanation
Indices: 397665--397745 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
397655 ATTTAGATTT
*
397665 AAATTTTTGAATATTTTTAATTAAACTCTCTC
1 AAATTTTT-AAAATTTTTAATTAAACTCTCTC
* *
397697 ATGATTTTTAAAATTTCTT-ATTAAGCT-TCTC
1 A-AATTTTTAAAATTT-TTAATTAAACTCTCTC
*
397728 AAATTTTTAAAATGTTTA
1 AAATTTTTAAAATTTTTA
397746 GCTACTCTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
29 2 0.05
30 12 0.29
31 5 0.12
32 14 0.34
33 8 0.20
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.51
Consensus pattern (31 bp):
AAATTTTTAAAATTTTTAATTAAACTCTCTC
Found at i:398957 original size:20 final size:20
Alignment explanation
Indices: 398936--398972 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
398926 ATTTTTGATA
398936 AAAATATAT-ATAATTTTTT
1 AAAATATATAATAATTTTTT
398955 AAAATATATAATAATTTT
1 AAAATATATAATAATTTT
398973 AAATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATATATAATAATTTTTT
Found at i:398976 original size:17 final size:17
Alignment explanation
Indices: 398941--398975 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
398931 TGATAAAAAT
*
398941 ATATATAATTTTTTAAA
1 ATATATAATATTTTAAA
398958 ATATATAATAATTTTAAA
1 ATATATAAT-ATTTTAAA
398976 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATAATATTTTAAA
Found at i:407546 original size:20 final size:21
Alignment explanation
Indices: 407507--407550 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
407497 AAAATACAAA
407507 AAAAATTCAGTAAAACATATAT
1 AAAAATTCA-TAAAACATATAT
*
407529 AAAAATTC-TAAAATATATAT
1 AAAAATTCATAAAACATATAT
407549 AA
1 AA
407551 TAACTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAATTCATAAAACATATAT
Found at i:417298 original size:49 final size:49
Alignment explanation
Indices: 417226--417329 Score: 199
Period size: 49 Copynumber: 2.1 Consensus size: 49
417216 CAATCTTCAT
417226 TGAGCATCTTGGAGAGATGGATTTCCTACCATATCCTTTCACTATCTCC
1 TGAGCATCTTGGAGAGATGGATTTCCTACCATATCCTTTCACTATCTCC
*
417275 TGAGCATCTTGGAGAGATGGATTTCCTACTATATCCTTTCACTATCTCC
1 TGAGCATCTTGGAGAGATGGATTTCCTACCATATCCTTTCACTATCTCC
417324 TGAGCA
1 TGAGCA
417330 AGAAGAGCAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (49 bp):
TGAGCATCTTGGAGAGATGGATTTCCTACCATATCCTTTCACTATCTCC
Found at i:435367 original size:21 final size:21
Alignment explanation
Indices: 435343--435419 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
435333 TATCGCAAAT
*
435343 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
435364 TCGCGTTGCGCT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
435384 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
435405 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
435420 CTACAGTTGT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:435548 original size:6 final size:6
Alignment explanation
Indices: 435537--435563 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
435527 GACACGTATT
435537 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
435564 CGAGACTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:436225 original size:19 final size:19
Alignment explanation
Indices: 436201--436286 Score: 75
Period size: 19 Copynumber: 4.4 Consensus size: 19
436191 CAACGAATTT
436201 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
436220 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
*
436242 TAGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* *
436261 TCGCAACGAA-ATGAAAAA
1 TCGCAACGAATTTGGAAAA
436279 TCGCAACG
1 TCGCAACG
436287 CGATTTTCAA
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
18 14 0.27
19 22 0.42
20 2 0.04
21 2 0.04
22 12 0.23
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:445020 original size:36 final size:36
Alignment explanation
Indices: 444973--445047 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
444963 TTTCATATTT
444973 TCCAGATTTCCCTTCTCCAACAACCCAACTTCCAAC
1 TCCAGATTTCCCTTCTCCAACAACCCAACTTCCAAC
445009 TCCAGATTTCCCTTCTCCAACAACCCAACTTCCAAC
1 TCCAGATTTCCCTTCTCCAACAACCCAACTTCCAAC
445045 TCC
1 TCC
445048 GATCTACTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.27, C:0.45, G:0.03, T:0.25
Consensus pattern (36 bp):
TCCAGATTTCCCTTCTCCAACAACCCAACTTCCAAC
Found at i:445584 original size:13 final size:13
Alignment explanation
Indices: 445583--445619 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
445573 CCGTTTACCC
*
445583 GACCCGACCTGTT
1 GACCCGACCCGTT
*
445596 TACCCGACCCGTT
1 GACCCGACCCGTT
445609 GACCCGACCCG
1 GACCCGACCCG
445620 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:445584 original size:18 final size:18
Alignment explanation
Indices: 445561--445606 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
445551 ACCGGTCACA
445561 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
*
445579 ACCCGACCCGACCTGTTT
1 ACCCGACCCGACCCGTTT
445597 ACCCGACCCG
1 ACCCGACCCG
445607 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:445618 original size:18 final size:18
Alignment explanation
Indices: 445561--445634 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 18
445551 ACCGGTCACA
*
445561 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
445579 ACCCGACCCGACCTGTT-
1 ACCCGACCCGACCCGTTG
*
445596 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
445610 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
445628 ACTCGAC
1 ACCCGAC
445635 ACGTTGACCG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
13 11 0.24
18 35 0.76
ACGTcount: A:0.18, C:0.47, G:0.19, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:445640 original size:31 final size:31
Alignment explanation
Indices: 445565--445643 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
445555 GTCACAACCC
* *
445565 GACCCGACCCGTTTACCCGACCCGACCTGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
445596 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
445627 GACTCGACACGTTGACC
1 GACCCGACCCGTTGACC
445644 GTTGACTGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.18, C:0.44, G:0.20, T:0.18
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:446955 original size:18 final size:18
Alignment explanation
Indices: 446929--446963 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
446919 TCGAAAGGAC
*
446929 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
446947 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
446964 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:453669 original size:2 final size:2
Alignment explanation
Indices: 453664--453702 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
453654 TACACACATT
453664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
453703 GATGAGCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:454330 original size:60 final size:60
Alignment explanation
Indices: 454237--454395 Score: 273
Period size: 60 Copynumber: 2.6 Consensus size: 60
454227 GCACGCTGGG
**
454237 CTAAGTAACAAATATTACCTACATCGGTAATTAGGCTTTCATGCGATTACCTAAATTTCC
1 CTAAGTAACAACGATTACCTACATCGGTAATTAGGCTTTCATGCGATTACCTAAATTTCC
* * *
454297 CTAAGTAACAACGGTTACCTACATCGGTAATTAGGTTTTCATGCGATTACCTAAATTTTC
1 CTAAGTAACAACGATTACCTACATCGGTAATTAGGCTTTCATGCGATTACCTAAATTTCC
454357 CTAAGTAACAACGATTACCTACATCGGTAATTAGGCTTT
1 CTAAGTAACAACGATTACCTACATCGGTAATTAGGCTTT
454396 TTAACTACGC
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (60 bp):
CTAAGTAACAACGATTACCTACATCGGTAATTAGGCTTTCATGCGATTACCTAAATTTCC
Found at i:459033 original size:24 final size:24
Alignment explanation
Indices: 458996--459055 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
458986 ACAACACTAA
*
458996 ATGAACGT-TAAACGAACATGTTC
1 ATGAACATATAAACGAACATGTTC
459019 ATGAACATATAAACGAACATGTTC
1 ATGAACATATAAACGAACATGTTC
*
459043 GTGAACATATAAA
1 ATGAACATATAAA
459056 TGAATGCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 7 0.21
24 27 0.79
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (24 bp):
ATGAACATATAAACGAACATGTTC
Found at i:459067 original size:59 final size:58
Alignment explanation
Indices: 458988--459118 Score: 208
Period size: 59 Copynumber: 2.2 Consensus size: 58
458978 ACACTAAAAC
* * * *
458988 AACACTAAATGAACGTTAAACGAACATGTTCATGAACATATAAACGAACATGTTCGTG
1 AACATTAAATGAACGCTAAACGAACATGTTCATGAACATATAAACAAACATGTTCGCG
*
459046 AACATATAAATGAATGCTAAACGAACATGTTCATGAACATATAAACAAACATGTTCGCG
1 AACAT-TAAATGAACGCTAAACGAACATGTTCATGAACATATAAACAAACATGTTCGCG
459105 AACATTAAATGAAC
1 AACATTAAATGAAC
459119 ATATTCGTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 12 0.18
59 54 0.82
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (58 bp):
AACATTAAATGAACGCTAAACGAACATGTTCATGAACATATAAACAAACATGTTCGCG
Found at i:459096 original size:24 final size:24
Alignment explanation
Indices: 459063--459136 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 24
459053 AAATGAATGC
*
459063 TAAACGAACATGTTCATGAACATA
1 TAAACGAACATGTTCGTGAACATA
* *
459087 TAAACAAACATGTTCGCGAACAT-
1 TAAACGAACATGTTCGTGAACATA
* *
459110 TAAATGAACATATTCGTGAACA-A
1 TAAACGAACATGTTCGTGAACATA
459133 TAAA
1 TAAA
459137 TAAATGAACA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 22 0.52
24 20 0.48
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (24 bp):
TAAACGAACATGTTCGTGAACATA
Found at i:461715 original size:60 final size:60
Alignment explanation
Indices: 461584--461716 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
461574 GTTGAATGAT
* * * *
461584 CATTTTGTAACTTTTAATAGTTGATGGACTCAATAAAGCAACACTCTATAGTCAGAGGAT
1 CATTTTGTAATTTTTAATAGTCGATGGACTCAATAAAGCAACACTCTATAATCAGAGGAC
* * * *
461644 CATTTTATAATTTTTAATAGTCGA-GCGACTTAATCAAGCAATA-TCATATAATCAG-GGAC
1 CATTTTGTAATTTTTAATAGTCGATG-GACTCAATAAAGCAACACTC-TATAATCAGAGGAC
461703 CATTTATGTAATTT
1 CATTT-TGTAATTT
461717 ATTCTTTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
59 11 0.18
60 50 0.82
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (60 bp):
CATTTTGTAATTTTTAATAGTCGATGGACTCAATAAAGCAACACTCTATAATCAGAGGAC
Found at i:462575 original size:20 final size:20
Alignment explanation
Indices: 462550--462879 Score: 228
Period size: 20 Copynumber: 16.6 Consensus size: 20
462540 TAGTTGAAAA
*
462550 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
462570 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
462590 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
462610 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* **
462630 TCGCGTTGCGATAGTCTATAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
462652 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* * *
462673 T--TGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
462693 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
**
462714 T--CGTTGCGA------AAA
1 TCGCGTTGCGATTTTCCAGT
462726 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
**
462746 TCGCGTTGCGATAGTCAACAGT
1 TCGCGTTGCGATTTTC--CAGT
*
462768 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* *
462789 T--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
462809 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
*
462830 T--CGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
462848 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
462868 TCGCGTTGCGAT
1 TCGCGTTGCGAT
462880 AGTTGAAAAT
Statistics
Matches: 250, Mismatches: 32, Indels: 56
0.74 0.09 0.17
Matches are distributed among these distances:
12 3 0.01
14 8 0.03
18 3 0.01
19 39 0.16
20 129 0.52
21 20 0.08
22 48 0.19
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:462658 original size:22 final size:21
Alignment explanation
Indices: 462633--462704 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
462623 TTCCAGTTCG
462633 CGTTGCGATAGTCTATAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
** * *
462655 CGTTGCGATTTTCCAAATT-T
1 CGTTGCGATAGTCTAAGTTGT
462675 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
462696 CGTTGCGAT
1 CGTTGCGAT
462705 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (21 bp):
CGTTGCGATAGTCTAAGTTGT
Found at i:462680 original size:19 final size:19
Alignment explanation
Indices: 462656--462722 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
462646 TATAGTTGTC
462656 GTTGCGATTTTCCAAATTT
1 GTTGCGATTTTCCAAATTT
** * *
462675 GTTGCGATAGTCTACAGTTGT
1 GTTGCGATTTTCCA-AATT-T
*
462696 CGTTGCGATTTTCCAAATTC
1 -GTTGCGATTTTCCAAATTT
462716 GTTGCGA
1 GTTGCGA
462723 AAATCGCGTT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
19 18 0.50
20 3 0.08
21 4 0.11
22 11 0.31
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.40
Consensus pattern (19 bp):
GTTGCGATTTTCCAAATTT
Found at i:462694 original size:41 final size:41
Alignment explanation
Indices: 462613--462839 Score: 294
Period size: 41 Copynumber: 5.7 Consensus size: 41
462603 TTCCAGTTCG
* *
462613 CGTTGCGATTTTCC-AGTTCGCGTTGCGATAGTCTATAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
*
462655 CGTTGCGATTTTCCAAATTTGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
*
462696 CGTTGCGATTTTCCAAATTCGTTGCGA-A----A-A-TCG-
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
* *
462729 CGTTGCGATTTTCC-AGTTCGCGTTGCGATAGTCAACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
462771 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
462812 CGTTGCGATTTTCCAAATTCGTTGCGAT
1 CGTTGCGATTTTCCAAATTCGTTGCGAT
462840 TTTCCATTTC
Statistics
Matches: 164, Mismatches: 9, Indels: 25
0.83 0.05 0.13
Matches are distributed among these distances:
32 3 0.02
33 14 0.09
34 10 0.06
35 2 0.01
36 1 0.01
39 1 0.01
40 2 0.01
41 97 0.59
42 28 0.17
43 6 0.04
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:462740 original size:116 final size:117
Alignment explanation
Indices: 462610--462882 Score: 449
Period size: 116 Copynumber: 2.3 Consensus size: 117
462600 ATTTTCCAGT
* * *
462610 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTATAGTTGTCGTTGCGATTTTCCAAATTT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCAACAGTTGTCGTTGCGATTTTCCAAATTC
462675 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGA-AAA
66 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAAA
462726 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCAACAGTTGTCGTTGCGATTTTCCAAATTC
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCAACAGTTGTCGTTGCGATTTTCCAAATTC
**
462791 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATTTTCCATT
66 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGA---T--AAA
462848 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
462883 TGAAAATCGA
Statistics
Matches: 146, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
116 110 0.75
122 36 0.25
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (117 bp):
TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCAACAGTTGTCGTTGCGATTTTCCAAATTC
GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAAA
Found at i:462774 original size:22 final size:22
Alignment explanation
Indices: 462749--462820 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
462739 TTCCAGTTCG
462749 CGTTGCGATAGTCAACAGTTGT
1 CGTTGCGATAGTCAACAGTTGT
**
462771 CGTTGCGATTTTCCAA-A--T-T
1 CGTTGCGATAGT-CAACAGTTGT
*
462790 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCAACAGTTGT
462812 CGTTGCGAT
1 CGTTGCGAT
462821 TTTCCAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 2 0.05
19 12 0.30
20 1 0.03
21 1 0.03
22 21 0.52
23 3 0.08
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCAACAGTTGT
Found at i:462794 original size:19 final size:19
Alignment explanation
Indices: 462770--462865 Score: 95
Period size: 19 Copynumber: 4.8 Consensus size: 19
462760 TCAACAGTTG
462770 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
462789 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
462810 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
*
462830 TCGTTGCGATTTTCC-ATT
1 TCGTTGCGATTTTCCAAAT
462848 TCGCGTTGCGATTTTCCA
1 T--CGTTGCGATTTTCCA
462866 GTTCGCGTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
18 3 0.05
19 25 0.40
20 19 0.31
21 5 0.08
22 10 0.16
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:464806 original size:2 final size:2
Alignment explanation
Indices: 464801--464836 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
464791 TATCTGGAAA
464801 AT AT AT AT -T AT -T AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
464837 ATAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:481496 original size:2 final size:2
Alignment explanation
Indices: 481489--481554 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
481479 ACACTTCGAG
481489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
481531 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
481555 CATTTGATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:482162 original size:21 final size:20
Alignment explanation
Indices: 482125--482163 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
482115 CCCATAGTAA
*
482125 AATTTGAGATTATGGTTAGG
1 AATTTGAGATTAGGGTTAGG
*
482145 AATTTGGGTATTAGGGTTA
1 AATTTGAG-ATTAGGGTTA
482164 AGGATTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (20 bp):
AATTTGAGATTAGGGTTAGG
Found at i:490833 original size:50 final size:50
Alignment explanation
Indices: 490778--490874 Score: 176
Period size: 50 Copynumber: 1.9 Consensus size: 50
490768 AATATTTATT
* *
490778 TATGATTTTTATGAATTTTAATGTATTTATCAAGTTAAGATTTATGAAAA
1 TATGATTTTTAGGAATTTTAATGTATTTATCAAATTAAGATTTATGAAAA
490828 TATGATTTTTAGGAATTTTAATGTATTTATCAAATTAAGATTTATGA
1 TATGATTTTTAGGAATTTTAATGTATTTATCAAATTAAGATTTATGA
490875 TTTAAGGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.48
Consensus pattern (50 bp):
TATGATTTTTAGGAATTTTAATGTATTTATCAAATTAAGATTTATGAAAA
Found at i:503624 original size:10 final size:10
Alignment explanation
Indices: 503609--503643 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
503599 TATACCACTT
503609 AAAATATAAA
1 AAAATATAAA
503619 AAAATATAAA
1 AAAATATAAA
*
503629 TAAATATAAA
1 AAAATATAAA
503639 TAAAA
1 -AAAA
503644 AATATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 19 0.86
11 3 0.14
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAATATAAA
Found at i:503641 original size:24 final size:25
Alignment explanation
Indices: 503608--503664 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
503598 ATATACCACT
503608 TAAAATATAAAAAAATATAAATA-AA
1 TAAAA-ATAAAAAAATATAAATATAA
* *
503633 TATAAAT-AAAAAATATAATTATAA
1 TAAAAATAAAAAAATATAAATATAA
503657 TAAAAATA
1 TAAAAATA
503665 TAATTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 13 0.48
24 10 0.37
25 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (25 bp):
TAAAAATAAAAAAATATAAATATAA
Found at i:503646 original size:17 final size:17
Alignment explanation
Indices: 503626--503677 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
503616 AAAAAAATAT
503626 AAATAAA-TATAAATAAA
1 AAATAAATTAT-AATAAA
503643 AAATATAATTATAATAAA
1 AAATA-AATTATAATAAA
*
503661 AATATAATTTATAATAA
1 AA-ATAAATTATAATAA
503678 CTCACTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 5 0.16
18 20 0.65
19 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAATTATAATAAA
Found at i:503660 original size:18 final size:19
Alignment explanation
Indices: 503637--503677 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 19
503627 AATAAATATA
503637 AATAAAAAATATAA-TTAT
1 AATAAAAAATATAATTTAT
503655 AAT-AAAAATATAATTTAT
1 AATAAAAAATATAATTTAT
503673 AATAA
1 AATAA
503678 CTCACTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
18 10 0.48
19 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAAAAAATATAATTTAT
Found at i:511229 original size:5 final size:5
Alignment explanation
Indices: 511219--511243 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
511209 TGATATCTGA
511219 TTGAT TTGAT TTGAT TTGAT TTGAT
1 TTGAT TTGAT TTGAT TTGAT TTGAT
511244 GCAGATGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TTGAT
Found at i:514836 original size:4 final size:4
Alignment explanation
Indices: 514827--514851 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
514817 AAACATTCAC
514827 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
514852 TATATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:519033 original size:2 final size:2
Alignment explanation
Indices: 519026--519050 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
519016 TTGATGTGAC
519026 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
519051 GCTCAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:523530 original size:38 final size:38
Alignment explanation
Indices: 523477--523550 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
523467 ATCCAACTCG
*
523477 ATTCGAAAATCATATATTATTCATTTAATTTGAATTTA
1 ATTCGAAAATCATATATTATTCATTCAATTTGAATTTA
* *
523515 ATTCGAAAAAT-ATATATTATTTATTCGATTTGAATT
1 ATTCG-AAAATCATATATTATTCATTCAATTTGAATT
523551 CGACCTGTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 27 0.84
39 5 0.16
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (38 bp):
ATTCGAAAATCATATATTATTCATTCAATTTGAATTTA
Found at i:523552 original size:33 final size:37
Alignment explanation
Indices: 523477--523553 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 37
523467 ATCCAACTCG
*
523477 ATTCGAAAATCATATATTATTCATTTAATTTGAATTTA
1 ATTCGAAAA-CATATATTATTCATTTAATTCGAATTTA
523515 ATTCGAAAA-ATATA-TATT-ATTT-ATTCG-ATTTGA
1 ATTCGAAAACATATATTATTCATTTAATTCGAATTT-A
523548 ATTCGA
1 ATTCGA
523554 CCTGTCTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
32 4 0.11
33 11 0.30
34 4 0.11
35 4 0.11
36 5 0.14
38 9 0.24
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (37 bp):
ATTCGAAAACATATATTATTCATTTAATTCGAATTTA
Found at i:527783 original size:22 final size:22
Alignment explanation
Indices: 527755--527806 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
527745 GCTTTGCATG
527755 CGCCATGCACGTCGGAAGAGGT
1 CGCCATGCACGTCGGAAGAGGT
527777 CGCCATGCACGTCGGAAGAGGT
1 CGCCATGCACGTCGGAAGAGGT
527799 CGCC-TGCA
1 CGCCATGCA
527807 TGGAGTGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.21, C:0.31, G:0.35, T:0.13
Consensus pattern (22 bp):
CGCCATGCACGTCGGAAGAGGT
Found at i:527884 original size:29 final size:29
Alignment explanation
Indices: 527852--527910 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
527842 AGGGCGCAGG
* *
527852 ACAAGGTCGCCCAGCGTGCATGGCGACCT
1 ACAAGGTCGCCCAGAGGGCATGGCGACCT
*
527881 ACAAGGTCGCCCGGAGGGCATGGCGACCT
1 ACAAGGTCGCCCAGAGGGCATGGCGACCT
527910 A
1 A
527911 TGCTGGGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.32, G:0.34, T:0.12
Consensus pattern (29 bp):
ACAAGGTCGCCCAGAGGGCATGGCGACCT
Found at i:533069 original size:36 final size:36
Alignment explanation
Indices: 533028--533103 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
533018 ATTTTCGGGA
*
533028 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
533064 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
533100 TTTT
1 TTTT
533104 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:533545 original size:15 final size:15
Alignment explanation
Indices: 533525--533554 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
533515 TATCACAATC
533525 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
533540 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
533555 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:538069 original size:36 final size:36
Alignment explanation
Indices: 538028--538103 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
538018 ATTTTCGGGA
*
538028 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
538064 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
538100 TTTT
1 TTTT
538104 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:539168 original size:15 final size:16
Alignment explanation
Indices: 539150--539201 Score: 70
Period size: 15 Copynumber: 3.1 Consensus size: 16
539140 TCAAACTATA
539150 ATAAAAATAAAAA-AT
1 ATAAAAATAAAAATAT
539165 ATAAAAATAAAAATAT
1 ATAAAAATAAAAATAT
539181 ATAATTATAATAAAAATAT
1 ATAA--A-AATAAAAATAT
539200 AT
1 AT
539202 TTTGTATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.39
16 6 0.18
18 1 0.03
19 13 0.39
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATAAAAATAT
Found at i:539170 original size:8 final size:8
Alignment explanation
Indices: 539150--539200 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
539140 TCAAACTATA
539150 ATAAAAAT
1 ATAAAAAT
539158 A-AAAAAT
1 ATAAAAAT
539165 ATAAAAAT
1 ATAAAAAT
539173 A-AAAATAT
1 ATAAAA-AT
**
539181 ATAATTAT
1 ATAAAAAT
539189 AATAAAAAT
1 -ATAAAAAT
539198 ATA
1 ATA
539201 TTTTGTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 11 0.31
8 16 0.46
9 8 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
ATAAAAAT
Found at i:539210 original size:17 final size:19
Alignment explanation
Indices: 539146--539201 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
539136 CAATTCAAAC
* *
539146 TATAATAAAAATAAAAAAT
1 TATAATAAAAATATATAAT
*
539165 ATAAAAATAAAAATATATAAT
1 -T-ATAATAAAAATATATAAT
539186 TATAATAAAAATATAT
1 TATAATAAAAATATAT
539202 TTTGTATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 14 0.45
20 2 0.06
21 15 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TATAATAAAAATATATAAT
Found at i:547413 original size:45 final size:45
Alignment explanation
Indices: 547363--547450 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
547353 GTCTACTTGA
547363 CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAACAT
1 CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAACAT
547408 CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAAC
1 CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAAC
547451 TTACACTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (45 bp):
CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAACAT
Found at i:548554 original size:16 final size:16
Alignment explanation
Indices: 548533--548571 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
548523 ACTTTTGGTT
548533 TAAACCTAGAATCGAC
1 TAAACCTAGAATCGAC
*
548549 TAAACCTAGAATCGGC
1 TAAACCTAGAATCGAC
548565 TAAACCT
1 TAAACCT
548572 TAGCTCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.21
Consensus pattern (16 bp):
TAAACCTAGAATCGAC
Found at i:549612 original size:18 final size:19
Alignment explanation
Indices: 549586--549630 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
549576 AATTAATCAC
549586 TTATGATCACATA-TCACAT
1 TTAT-ATCACATAGTCACAT
549605 TTATATCACATAGTCACAT
1 TTATATCACATAGTCACAT
549624 TTCATAT
1 TT-ATAT
549631 TTCACTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.33
19 12 0.50
20 4 0.17
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (19 bp):
TTATATCACATAGTCACAT
Found at i:558559 original size:2 final size:2
Alignment explanation
Indices: 558552--558609 Score: 63
Period size: 2 Copynumber: 31.5 Consensus size: 2
558542 CCGCCTCGAT
* *
558552 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T- TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
558592 TA -A T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA T
558610 TTTATTTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
1 5 0.10
2 43 0.90
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:558634 original size:25 final size:25
Alignment explanation
Indices: 558572--558634 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
558562 TATATATATA
*
558572 TATATTTA-TATATTTTATATTAAT
1 TATATTAATTATATTTTATATTAAT
* *
558596 TATA-TATATAATATTTTAT-TTATTT
1 TATATTA-ATTATATTTTATATTA-AT
558621 TATATTAATTATAT
1 TATATTAATTATAT
558635 ATATAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
23 1 0.03
24 8 0.26
25 20 0.65
26 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATATTAATTATATTTTATATTAAT
Found at i:558646 original size:34 final size:34
Alignment explanation
Indices: 558560--558647 Score: 149
Period size: 34 Copynumber: 2.5 Consensus size: 34
558550 ATTATATATA
558560 TATATATATATATATATTTATATATTTTATATTAAT
1 TATATATATA-ATAT-TTTATATATTTTATATTAAT
*
558596 TATATATATAATATTTTATTTATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
558630 TATATATATAATATTTTA
1 TATATATATAATATTTTA
558648 GGGTTCGGGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
34 37 0.73
35 4 0.08
36 10 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:558686 original size:25 final size:27
Alignment explanation
Indices: 558636--558687 Score: 90
Period size: 25 Copynumber: 2.0 Consensus size: 27
558626 TAATTATATA
558636 TATAATATTTTAGGGTTCGGGTTTGAG
1 TATAATATTTTAGGGTTCGGGTTTGAG
558663 TATAATATTTT-GGG-TCGGGTTTGAG
1 TATAATATTTTAGGGTTCGGGTTTGAG
558688 GACGGGGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 11 0.44
26 3 0.12
27 11 0.44
ACGTcount: A:0.21, C:0.04, G:0.31, T:0.44
Consensus pattern (27 bp):
TATAATATTTTAGGGTTCGGGTTTGAG
Found at i:560035 original size:6 final size:6
Alignment explanation
Indices: 560026--560056 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
560016 ATTATTACTA
560026 TTATAT TTATAT TTATAT TTATAT TT-TAT TT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TT
560057 TAATTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTATAT
Found at i:561262 original size:31 final size:30
Alignment explanation
Indices: 561191--561268 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
561181 ATTAATAAAT
* *
561191 ATATTTAACAAATTAGTCATAATGTTATCG
1 ATATGTAACAAATTAGTCATAACGTTATCG
* * *
561221 ATTTGAAACAAATT-GTTCACTAACGTTATTG
1 ATATGTAACAAATTAG-TCA-TAACGTTATCG
561252 ATATGTAACAAATTAGT
1 ATATGTAACAAATTAGT
561269 AATTAGTGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 1 0.03
30 14 0.37
31 22 0.58
32 1 0.03
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (30 bp):
ATATGTAACAAATTAGTCATAACGTTATCG
Found at i:561547 original size:15 final size:15
Alignment explanation
Indices: 561527--561629 Score: 109
Period size: 15 Copynumber: 6.5 Consensus size: 15
561517 TAATAAGGTT
561527 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
561542 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
561557 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
561572 ATTTATTATAAAATATGAA
1 ATTTATT-TTAAA-AT--A
*
561591 TTGATTTATTTTTAAATA
1 ---ATTTATTTTAAAATA
561609 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
561623 ATTTATT
1 ATTTATT
561630 AGTATGGATT
Statistics
Matches: 76, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
14 12 0.16
15 44 0.58
16 4 0.05
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 3 0.04
22 7 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:561563 original size:30 final size:30
Alignment explanation
Indices: 561527--561586 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
561517 TAATAAGGTT
561527 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
561557 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
561587 TGAATTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTATAAAATA
Found at i:561607 original size:22 final size:22
Alignment explanation
Indices: 561572--561676 Score: 61
Period size: 22 Copynumber: 4.7 Consensus size: 22
561562 TTTTAAAATA
* *
561572 ATTTATTATAAAATATGAATTG
1 ATTTATTTTTAAATATGAATTG
* * *
561594 ATTTATTTTTAAATAATTTATTTTA
1 ATTTATTTTTAAAT-A-TGA-ATTG
* * * *
561619 AATAATTTATT-AGTATGGATTG
1 ATTTATTT-TTAAATATGAATTG
* *
561641 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTTAAATATGAATTG
561663 ATTTA-TTTTAAATA
1 ATTTATTTTTAAATA
561677 ATTTATTAGT
Statistics
Matches: 61, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
21 9 0.15
22 35 0.57
23 2 0.03
24 3 0.05
25 10 0.16
26 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
ATTTATTTTTAAATATGAATTG
Found at i:561619 original size:14 final size:14
Alignment explanation
Indices: 561594--561629 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
561584 ATATGAATTG
561594 ATTTATTTTTAAATA
1 ATTTA-TTTTAAATA
561609 ATTTATTTTAAATA
1 ATTTATTTTAAATA
561623 ATTTATT
1 ATTTATT
561630 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:561647 original size:32 final size:32
Alignment explanation
Indices: 561609--561760 Score: 155
Period size: 32 Copynumber: 5.4 Consensus size: 32
561599 TTTTTAAATA
561609 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
561641 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
561663 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
561695 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
561717 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
561749 ATTTATTTTAAA
1 ATTTATTTTAAA
561761 ATATGGATTG
Statistics
Matches: 99, Mismatches: 1, Indels: 40
0.71 0.01 0.29
Matches are distributed among these distances:
22 28 0.28
23 8 0.08
25 2 0.02
26 6 0.06
28 6 0.06
29 2 0.02
31 8 0.08
32 39 0.39
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:561663 original size:69 final size:67
Alignment explanation
Indices: 561527--561684 Score: 203
Period size: 69 Copynumber: 2.3 Consensus size: 67
561517 TAATAAGGTT
*
561527 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGAAT
1 ATTTATTTTTAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGAAT
561592 TG
66 TG
* ** * * *
561594 ATTTATTTTTAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 ATTTATTTTTAAATAATTTATTATAAAATAATTTATT--T-TAAAATAATTTATTATAAAATATG
*
561658 GATTG
63 AATTG
561663 ATTTA-TTTTAAATAATTTATTA
1 ATTTATTTTTAAATAATTTATTA
561685 GTATGGATTG
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
66 13 0.16
67 21 0.27
68 17 0.22
69 28 0.35
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (67 bp):
ATTTATTTTTAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGAAT
TG
Found at i:561675 original size:54 final size:54
Alignment explanation
Indices: 561609--562201 Score: 592
Period size: 54 Copynumber: 11.1 Consensus size: 54
561599 TTTTTAAATA
561609 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
561663 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
561717 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
561771 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * ***
561815 ATTTGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
561877 ATTTATTTTAAATAATTTATTAGTATGGA-TGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
561930 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTTAGTATGAATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT--A-AA----A-TATGGATTG
* * * * *** **
561986 ATTTATTTT-AA-AA--TA-T-GGATTGATTTA-TTATTGTAGTTGTATAAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTG
*
562034 ATTTA-TTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
562087 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
562141 ATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
562195 ATTTATT
1 ATTTATT
562202 ATTGTAGTTG
Statistics
Matches: 450, Mismatches: 47, Indels: 84
0.77 0.08 0.14
Matches are distributed among these distances:
44 7 0.02
46 1 0.00
47 18 0.04
48 50 0.11
49 6 0.01
50 6 0.01
51 8 0.02
52 3 0.01
53 34 0.08
54 241 0.54
55 10 0.02
56 25 0.06
57 8 0.02
58 11 0.02
59 3 0.01
60 2 0.00
62 17 0.04
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:561711 original size:22 final size:22
Alignment explanation
Indices: 561686--561728 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
561676 AATTTATTAG
561686 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
561708 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
561729 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:561832 original size:18 final size:18
Alignment explanation
Indices: 561785--561836 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
561775 ATTATTGTAG
*
561785 TTGTATGGATTGATTTAT
1 TTGTATGAATTGATTTAT
*
561803 TT-TA--AA-TAATTTAT
1 TTGTATGAATTGATTTAT
561817 TTGTATGAATTGATTTAT
1 TTGTATGAATTGATTTAT
561835 TT
1 TT
561837 TAAAATATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.33
15 3 0.11
17 4 0.15
18 11 0.41
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
TTGTATGAATTGATTTAT
Found at i:561958 original size:79 final size:80
Alignment explanation
Indices: 561708--562093 Score: 683
Period size: 80 Copynumber: 4.9 Consensus size: 80
561698 TATTTTAAAA
561708 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAAATATGGATTGA
561772 TTTATTATTGTAGTTG
65 TTTATTATTGTAGTTG
*
561788 TATGGATTGATTTATTTTAAATAATTTATTTGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
561853 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
561868 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGA-TGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
561932 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
561947 TATGGATTGATTTATTTTAAATAA-TT-TTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
562010 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
** *
562025 TATAAATTGATTTA-TTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
562089 TTATT
66 TTATT
562094 TTAAATAATT
Statistics
Matches: 295, Mismatches: 7, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
77 18 0.06
78 57 0.19
79 106 0.36
80 113 0.38
81 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:562067 original size:157 final size:159
Alignment explanation
Indices: 561713--562093 Score: 680
Period size: 157 Copynumber: 2.4 Consensus size: 159
561703 TAAAATATGG
561713 ATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGATTTATT
*
561778 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTTGTATGAATTGATTTATTTTAAAAT
65 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAAT
**
561843 ATGGATTGATTTATTATTGTAGTTGTATGG
130 ATGGATTGATTTATTATTGTAGTTGTATAA
561873 ATTGATTTATTTTAAATAATTTATTAGTATGGA-TGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGATTTATT
561937 ATTGTAGTTGTATGGATTGATTTATTTTAAATAA-TT-TTAGTATGAATTGATTTATTTTAAAAT
65 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAAT
562000 ATGGATTGATTTATTATTGTAGTTGTATAA
130 ATGGATTGATTTATTATTGTAGTTGTATAA
562030 ATTGATTTA-TTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAAATATGGATTGATTTATT
562094 TTAAATAATT
Statistics
Matches: 215, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
155 1 0.00
156 21 0.10
157 94 0.44
158 2 0.01
159 65 0.30
160 32 0.15
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (159 bp):
ATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGGATTGATTTATTA
TTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATA
TGGATTGATTTATTATTGTAGTTGTATAA
Found at i:562081 original size:22 final size:22
Alignment explanation
Indices: 562056--562098 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
562046 AATTTATTAG
562056 TATGCATTGATTTATTTTAAAA
1 TATGCATTGATTTATTTTAAAA
*
562078 TATGGATTGATTTATTTTAAA
1 TATGCATTGATTTATTTTAAA
562099 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGCATTGATTTATTTTAAAA
Found at i:562116 original size:32 final size:32
Alignment explanation
Indices: 562078--562184 Score: 126
Period size: 32 Copynumber: 3.7 Consensus size: 32
562068 TATTTTAAAA
562078 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
562110 TATGGATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
562132 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
562164 TATGGATTGGTTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
562185 ATATGGATTG
Statistics
Matches: 63, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
22 14 0.22
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 3 0.05
32 34 0.54
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:562135 original size:22 final size:22
Alignment explanation
Indices: 562110--562152 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
562100 AATTTATTAG
562110 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
562132 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
562153 TAATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:562228 original size:80 final size:80
Alignment explanation
Indices: 562132--562281 Score: 264
Period size: 80 Copynumber: 1.9 Consensus size: 80
562122 TATTTTAAAA
* * * *
562132 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
562197 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
562212 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
562277 TTATT
66 TTATT
562282 TTAAATAATT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
TTATTATTGTAGTTG
Found at i:562253 original size:134 final size:134
Alignment explanation
Indices: 561868--562295 Score: 581
Period size: 134 Copynumber: 3.2 Consensus size: 134
561858 ATTGTAGTTG
*
561868 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGA-TGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
561932 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAA-TT-TTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
561995 AAAA
131 AAAA
* * ** * *
561999 TATGGATTGATTTA--TT--AT--TGTAGTTGTATAAATTGATTTATTTAAATAATTTAT-TAGT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAA-AA--TATGGA-T
* * *** *
562057 ATGCATTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
62 -TG-ATTTA-TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
562121 TTATTTTAAAA
124 TTATTTTAAAA
*
562132 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
562197 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
562262 AAAA
131 AAAA
*
562266 TATAGATTGATTTATTTTAAATAATTTATT
1 TATGGATTGATTTATTTTAAATAATTTATT
562296 ATTGTAGTTG
Statistics
Matches: 252, Mismatches: 27, Indels: 33
0.81 0.09 0.11
Matches are distributed among these distances:
125 9 0.04
126 12 0.05
127 4 0.02
128 1 0.00
129 6 0.02
130 2 0.01
131 42 0.17
132 9 0.04
133 46 0.18
134 86 0.34
135 4 0.02
136 4 0.02
137 3 0.01
138 2 0.01
139 22 0.09
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
AAAA
Found at i:566875 original size:18 final size:18
Alignment explanation
Indices: 566852--566926 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
566842 ACCGGTCACA
566852 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
566870 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
566888 ACCTGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
566901 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
566919 ACCCGACC
1 ACCCGACC
566927 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:566902 original size:31 final size:31
Alignment explanation
Indices: 566856--566926 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
566846 GTCACAACCC
*
566856 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
* *
566887 TACCTGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
566918 GACCCGACC
1 GACCCGACC
566927 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (31 bp):
GACCCGACCCATTGACCCGACCCGACCCGTT
Found at i:566930 original size:12 final size:13
Alignment explanation
Indices: 566905--566948 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
566895 CCATTGACCC
566905 GACCCGACCCGTT
1 GACCCGACCCGTT
566918 GACCCGA-CCGTT
1 GACCCGACCCGTT
*
566930 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
566945 GACC
1 GACC
566949 ATTGACCGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 2 0.07
15 9 0.33
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:566935 original size:7 final size:7
Alignment explanation
Indices: 566923--566956 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
566913 CCGTTGACCC
566923 GACCGTT
1 GACCGTT
566930 GACCGTT
1 GACCGTT
566937 GACCCGTT
1 GA-CCGTT
*
566945 GACCATT
1 GACCGTT
566952 GACCG
1 GACCG
566957 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:566945 original size:15 final size:15
Alignment explanation
Indices: 566925--566955 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
566915 GTTGACCCGA
*
566925 CCGTTGACCGTTGAC
1 CCGTTGACCATTGAC
566940 CCGTTGACCATTGAC
1 CCGTTGACCATTGAC
566955 C
1 C
566956 GGAGTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCATTGAC
Found at i:568267 original size:18 final size:18
Alignment explanation
Indices: 568241--568275 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
568231 TCGAAAGGAC
*
568241 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
568259 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
568276 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:571992 original size:9 final size:9
Alignment explanation
Indices: 571978--572023 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
571968 AAGGAAAAAG
571978 TGACCGGTT
1 TGACCGGTT
571987 TGACCGGTTT
1 TGACCGG-TT
* *
571997 TGGAACTGTT
1 T-GACCGGTT
572007 TGACCGGTT
1 TGACCGGTT
572016 TGACCGGT
1 TGACCGGT
572024 CACAACCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 21 0.68
10 6 0.19
11 4 0.13
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.35
Consensus pattern (9 bp):
TGACCGGTT
Found at i:572051 original size:18 final size:18
Alignment explanation
Indices: 572028--572102 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 18
572018 ACCGGTCACA
572028 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
572046 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
* *
572064 ACCTGA--C--CCCATTG
1 ACCCGACCCGACCCGTTG
572078 ACCCGACCCGACCCG-TG
1 ACCCGACCCGACCCGTTG
572095 ACCCGACC
1 ACCCGACC
572103 GTTGACCGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
14 10 0.21
16 2 0.04
17 10 0.21
18 25 0.53
ACGTcount: A:0.19, C:0.51, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:572109 original size:7 final size:7
Alignment explanation
Indices: 572099--572132 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
572089 CCCGTGACCC
572099 GACCGTT
1 GACCGTT
572106 GACCGTT
1 GACCGTT
572113 GACCCGTT
1 GA-CCGTT
*
572121 GACCATT
1 GACCGTT
572128 GACCG
1 GACCG
572133 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:572121 original size:15 final size:15
Alignment explanation
Indices: 572101--572131 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
572091 CGTGACCCGA
*
572101 CCGTTGACCGTTGAC
1 CCGTTGACCATTGAC
572116 CCGTTGACCATTGAC
1 CCGTTGACCATTGAC
572131 C
1 C
572132 GGAGTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCATTGAC
Done.